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Integrative analysis of the melanoma transcriptome
Open accessAbstract
Global studies of transcript structure and abundance in cancer cells enable the systematic discovery of aberrations that contribute to carcinogenesis, including gene fusions, alternative splice isoforms, and somatic mutations. We developed a systematic approach to characterize the spectrum of cancer-associated mRNA alterations through integration of transcriptomic and structural genomic data, and we applied this approach to generate new insights into melanoma biology. Using paired-end massively parallel sequencing of cDNA (RNA-seq) together with analyses of high-resolution chromosomal copy number data, we identified 11 novel melanoma gene fusions produced by underlying genomic rearrangements, as well as 12 novel readthrough transcripts. We mapped these chimeric transcripts to base-pair resolution and traced them to their genomic origins using matched chromosomal copy number information. We also used these data to discover and validate base-pair mutations that accumulated in these melanomas, revealing a surprisingly high rate of somatic mutation and lending support to the notion that point mutations constitute the major driver of melanoma progression. Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types.
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“Over the last two years, with the further confirmation that the relatively short reads can be effectively assembled [15], especially with the great advantage of paired-end sequencing [54], the Illumina transcriptome or whole genome de novo sequencing and assembly have been successfully used for model [12,16,55-58]and non-model organisms [25-27,59].”
From De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) (2010) · cites this paper as [56]
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“This approach has led to important biological findings in oncolog”
Background
Metadata
- Authors
- Berger, M. F., Levin, J. Z., Vijayendran, K., Sivachenko, A., Adiconis, X., Maguire, J., Johnson, L. A., Robinson, J., Verhaak, R. G., Sougnez, C., Onofrio, R. C., Ziaugra, L., Cibulskis, K., Laine, E., Barretina, J., Winckler, W., Fisher, D. E., Getz, G., Meyerson, M., Jaffe, D. B., Gabriel, S. B., Lander, E. S., Dummer, R., Gnirke, A., Nusbaum, C., & Garraway, L. A.
- Affiliations
- Broad Institute (US)
- University Hospital Zurich (CH)
- Boston Children's Hospital (US)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2010-02-23
- Volume
- 20
- Issue
- 4
- Pages
- 413-427
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2847744
- OpenAlex
- W6948519597
- Cited by
- 305
- References
- 66
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 7 · 2023: 6 · 2022: 4 · 2021: 11 · 2020: 25 · 2019: 11 · 2018: 17 · 2017: 25 · 2016: 22 · 2015: 14 · 2014: 21 · 2013: 35 · 2012: 52
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- HighWire Press Open Archive (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- Dr. Miriam and Sheldon G. Adelson Medical Research Foundation
- Broad Institute
- National Human Genome Research Institute (U54HG003067)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01AR043369)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Health Sciences › Medicine › Oncology › Cutaneous Melanoma Detection and Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- melanoma, transcriptome, gene fusion, read-through transcripts, fusion transcripts, somatic mutations, chromosomal copy number alterations, alternative splicing, transcriptome integration, structural genomics, carcinogenesis, point mutations
- MeSH terms
- Base Sequence, DNA Mutational Analysis, Gene Amplification, Humans, Melanoma, Polymorphism, Genetic, Skin Neoplasms, Tumor Cells, Cultured, Gene Expression Regulation, Neoplastic, Matched-Pair Analysis, Sequence Analysis, DNA, Systems Integration, Gene Dosage, K562 Cells, Protein Isoforms, Gene Expression Profiling, Genomics, Gene Fusion
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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